In the days before David was king, Saul was jealous of David's growing power. Jonathan, however, knew it was God's will that David become king. Instead of being angry that he was no longer heir to the throne, he protected his friend David, the new heir, from the wrath of his father Saul. Jonathan tried to talk to his father, but when he realized he still wanted David dead, he gave David a secret verbal signal while shooting arrows outside so David would know to flee.

Once, when Jonathan and his armourbearer were in the wilderness of Michmash, they were discovered by a garrison of Philistines. On a "half acre of land, which a yoke of oxen might plow", the two of them killed twenty men.

Jonathan was slain in battle by the Philistines along with his father Saul at the Battle of Mount Gilboa. David wept bitterly for the loss of his friend. Jonathan was survived by a five-year-old son, Mephiboseth, who was crippled.